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R3
legacy
bedtools2
Commits
df1de0db
Commit
df1de0db
authored
May 16, 2015
by
arq5x
Browse files
Merge branch 'jmarshall-warnings3'
parents
66397856
b37d274d
Changes
6
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Makefile
View file @
df1de0db
...
...
@@ -179,7 +179,7 @@ $(UTIL_SUBDIRS) $(SUBDIRS): $(OBJ_DIR) $(BIN_DIR)
clean
:
@
$(MAKE)
--no-print-directory
--directory
=
$(BT_ROOT)
clean_api
@
echo
" * Cleaning up."
@
rm
-f
$(OBJ_DIR)
/
*
$(BIN_DIR)
/
*
@
rm
-f
$(VERSION_FILE)
$(OBJ_DIR)
/
*
$(BIN_DIR)
/
*
.PHONY
:
clean
test
:
all
...
...
src/closestFile/closestHelp.cpp
View file @
df1de0db
This diff is collapsed.
Click to expand it.
src/utils/FileRecordTools/Makefile
View file @
df1de0db
...
...
@@ -28,7 +28,10 @@ _EXT_OBJECTS=SingleLineDelimTextFileReader.o BamFileReader.o Bed3Interval.o Bed6
EXT_OBJECTS
=
$(
patsubst
%,
$(OBJ_DIR)
/%,
$(_EXT_OBJECTS)
)
BUILT_OBJECTS
=
$(
patsubst
%,
$(OBJ_DIR)
/%,
$(OBJECTS)
)
$(BUILT_OBJECTS)
:
$(SOURCES) $(SUBDIRS)
all
:
$(BUILT_OBJECTS) $(SUBDIRS)
.PHONY
:
all
$(BUILT_OBJECTS)
:
$(SOURCES)
@
echo
" * compiling FileRecordMgr.cpp"
@
$(CXX)
-c
-o
$(OBJ_DIR)
/FileRecordMgr.o FileRecordMgr.cpp
$(LDFLAGS)
$(CXXFLAGS)
$(INCLUDES)
@
echo
" * compiling FileRecordMergeMgr.cpp"
...
...
@@ -48,4 +51,4 @@ clean:
@
rm
-f
$(OBJ_DIR)
/FileRecordMergeMgr.o
.PHONY
:
clean
\ No newline at end of file
.PHONY
:
clean
src/utils/RecordOutputMgr/RecordOutputMgr.h
View file @
df1de0db
...
...
@@ -8,12 +8,12 @@
#ifndef RECORDOUTPUTMGR_H_
#define RECORDOUTPUTMGR_H_
using
namespace
std
;
#include
"ContextBase.h"
#include
"RecordKeyVector.h"
#include
"api/BamWriter.h"
using
namespace
std
;
class
BlockMgr
;
class
RecordOutputMgr
{
...
...
src/utils/general/CommonHelp.cpp
View file @
df1de0db
...
...
@@ -6,6 +6,8 @@
*/
#include
"CommonHelp.h"
using
namespace
std
;
void
CommonHelp
()
{
cerr
<<
"
\t
-iobuf
\t
"
<<
"Follow with desired integer size of read buffer."
<<
endl
;
cerr
<<
"
\t\t
"
<<
"Optional suffixes K/M/G supported."
<<
endl
;
...
...
src/utils/general/ParseTools.h
View file @
df1de0db
...
...
@@ -9,6 +9,7 @@
#define PARSETOOLS_H_
#include
<cstring>
//for memset
#include
<limits>
#include
<string>
#include
<vector>
#include
"QuickString.h"
...
...
@@ -37,8 +38,7 @@ int str2chrPos(const QuickString &str);
template
<
class
T
>
void
int2str
(
int
number
,
T
&
buffer
,
bool
appendToBuf
=
false
)
{
register
int
useNum
=
number
;
if
(
useNum
==
0
)
{
if
(
number
==
0
)
{
if
(
appendToBuf
)
{
buffer
.
append
(
"0"
);
}
else
{
...
...
@@ -47,42 +47,29 @@ void int2str(int number, T& buffer, bool appendToBuf = false)
return
;
}
//check for negative numbers.
bool
isNegative
=
useNum
<
0
;
bool
isNegative
=
number
<
0
;
register
unsigned
useNum
=
number
;
if
(
isNegative
)
{
useNum
=
0
-
useNum
;
//convert to positive.
}
//figure out how many digits we have
register
int
power
=
10
;
int
numChars
=
2
+
(
isNegative
?
1
:
0
);
while
(
power
<=
useNum
)
{
power
*=
10
;
numChars
++
;
}
char
tmpBuffer
[
numeric_limits
<
int
>::
digits10
+
3
];
char
*
tmpBuf
=
&
tmpBuffer
[
sizeof
tmpBuffer
];
*--
tmpBuf
=
'\0'
;
char
tmpBuf
[
numChars
];
memset
(
tmpBuf
,
0
,
numChars
);
while
(
useNum
>
0
)
{
*--
tmpBuf
=
(
useNum
%
10
)
+
'0'
;
useNum
/=
10
;
}
int
bufIdx
=
0
;
if
(
isNegative
)
{
tmpBuf
[
0
]
=
'-'
;
bufIdx
=
1
;
*--
tmpBuf
=
'-'
;
}
register
int
currDig
=
0
;
power
/=
10
;
while
(
power
)
{
currDig
=
useNum
/
power
;
useNum
-=
currDig
*
power
;
tmpBuf
[
bufIdx
]
=
currDig
+
48
;
//48 is ascii for zero.
bufIdx
++
;
power
/=
10
;
}
if
(
!
appendToBuf
)
{
buffer
=
tmpBuf
;
}
else
{
buffer
.
append
(
tmpBuf
,
numChars
-
1
);
buffer
.
append
(
tmpBuf
);
}
}
...
...
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